We use both "Sequencher" and Staden, depending on the
scale of the project.
If you are trying to create a mutation and doing
sequencing to verify the genetic engineering, "Sequencher"
is a good package to use.
However, if you are doing a large scale sequencing operation,
either a large region of a chromosome or cDNA library and you
want to automate not only the assembly, but also the searching
or "gene finding", then a package like Staden has a lot to
offer. We have added some post processing functions which
do homology searches for each sequence and then create
Mosaic pages of the search results.
Xbap, though functionally complete, was awkward
for our Mac users to use, and looks rather plain.
I'm sure that with the automated assembly routines
doing 90% of the work, some groups will eventually
use xbap to correct errors in the assembly, rather than
trying to do the whole project on the Mac.
I'm told the Staden package just under went a major revision.
The tape is on my shelf, not loaded yet ... .
You should also be aware of two other programs which are used
to assembly sequences. Phil Green has develop Phred and Phrack.
I forget which is which, but one of these programs is an improved
base calling program, that not only gives the base in the sequence
but also a statistically measure of how good the calling was. The other
program then assembles sequences, using these statistical measures.
Gene Meyers has developed an assembly program which handles repeats
quite well. In this package the number of sequences that cover
a region are counted. If this count is greater than the average
cover of the sequencing (like doing a 3x sequenching and coming
up with a region yield 6x or 9x coverage), then the program tries to
place multiple copies of the repeated region into the final sequence.
(Please forgive me for being a little loose with these program
descriptions but "being of little brain, long words bother me.")
